I was changing the transmission in my 08 Vue today and when I drained the pan I only took out 6 quarts, but the manuals indicates the transmission holds 9.5 quarts. How many miles should I drive before I drain another 3? Also, should I do it when the transmission is cold? Does the old fluid settle to the bottom?

As for settling out, the only thing that would settle out would be metal shavings on the magnetic drain plug. If you see those, you're in for a world of hurt.

Otherwise, the fluid is the fluid. I do not believe the specific gravity of the old fluid is different enough or that it is chemically different enough to become imimscible and sink to the bottom or separate.

The rest of the old tranny fluid was likely in the torque converter.
Don't know how to drain torque converter but sure it is out there
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New and old are now mixed together in a 2:1 ratio new to old--that's a fact
I don't feel like doing the math, but you'll continue to increase the ratio of clean to old fluid with additional changes.

If you're gonna bother pulling more, just pull the 6.5 again and refill.
Fluid will be cleaner than just pulling and replacing 3.

Continue ad nauseum until you feel you have sufficiently diluted away the old fluid.
____________If you can figure out how to drain the torque converter, do all 9.5 and you'll be done w it.